Faster, Cheaper Biomolecule Analysis

Over the past decade, Amit Meller, associate professor of biomedical engineering and physics, has used nanopores—akin to wedding rings but only one to five nanometers across—to detect and characterize DNA, RNA, and other biological molecules at the single-molecule level. The pores are sized at about the same scale as the cross-sections of the molecules they are to probe. Among other things, this technology could someday enable physicians to “read” the four bases of a sick patient’s DNA molecule as it is quickly threaded through the nanopore, enabling rapid mapping of large sections of that individual’s genome and a more precise treatment plan. Today Mellerís work promises to bring about dramatically faster and cheaper experimental methods in genomics, bioinformatics, and other biomedical disciplines.

An electrical field is used to draw negatively charged biopolymers, in this case DNA molecules, through a nanopore fabricated in an ultra-thin silicon substrate. Image courtesy of Amit Meller

An electrical field is used to draw negatively charged biopolymers, in this case DNA molecules, through a nanopore fabricated in an ultra-thin silicon substrate.
Image courtesy of Amit Meller

Using a high-end transmission electron microscope, Mellerís group punches the nanopores in extremely thin solid-state films and applies an electric field across the films as target molecules are threaded, one by one, through the nanopores. Upon entry, each molecule occludes some of the ion-current flowing through the pore and outputs a very distinct electrical signal. Within minutes the group can acquire and analyze signals from thousands of individual biomolecules. “This process allows us to distinguish different molecules, measure their lengths, and study how they interact with other biological molecules, such as DNA-binding proteins,” says Meller.

He now directs four major nanopore-related projects that could streamline several critical biomedical procedures. The first, funded by the NIH, uses nanopores in a high-throughput DNA sequencing method aimed at bringing down the cost of per-genome sequencing to $1,000. To achieve that goal, the group will use dense arrays of hundreds of nanopores, through which DNA segments will be threaded and read in parallel using optical signals.

“DNA sequencing requires millions of dollars and months of labor because the genome is so vast,” notes Meller. “The NIH envisions an under-$1,000-per-genome sequencing method to have a significant impact on health care and personalized medicine.” Another potential boon to personalized medicine, Mellerís second project uses nanopores to identify single-nucleotide differences between two genes. Pinpointing small variations between genomes could help physicians predict how individuals will react to specific drugs and therapies.

Amit Meller

Amit Meller

The two other projects could impact our understanding of the molecular machinery of biological processes in the cell, yielding knowledge of how genes are switched on or off, and producing new drugs to interfere with these processes.

Supported by the National Science Foundation (NSF), the third project explores how DNA molecules interact with transcription factors—proteins that bind to specific points on the DNA and regulate gene expression. “By examining the electronic signature of a single DNA molecule threaded through the nanopore, we hope to determine which transcription factors are bound to the DNA at a given time,” says Meller. The fourth project, supported by the Human Frontier Science Program, uses nanopores to apply mechanical forces on biological molecules, particularly mRNA, which tends to fold into complicated structures that determine its function within the cell. “By threading the mRNA molecule through a very small nanopore, we can unfold it and explore how it forms secondary structures,” Meller explains.